Molecular transport in individual pores (e.g., protein ion channels ((a) Kasianowicz, J. J.; Brandin, E.; Branton, D.; Deamer, D. W. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 13770; (b) Bayley, H; Cremer, P. S. Nature 2001, 413, 226; (c) Gu, L.-Q.; Braha, O.; Conlan, S.; Cheley, S. and Bayley, H. Nature 1999, 398, 686) and synthetic channels ((a) Ito, T.; Sun, L.; Crooks, R. M. Anal. Chem. 2003, 75, 2399; (b) Ito, T.; Sun. L.; Henriquez, R. R.; Crooks, R. M. Acc. Chem. Res. 2004, 37, 937; (c) Hinds, B. J.; Chopra, N.; Rantell, T.; Andrews, R.; Gavalas, V.; Bachas, L. G. Science 2004, 303, 62. (d) Majumber, M.; Chopra, N.; Hings, B. J. J. Am. Chem. Soc. 2005, 127, 9062; (e) Li, J.; Gershow, M.; Stein, D.; Brandin, D.; Golovchenko, J. A. Nat. Mater. 2003, 2, 611; (f) Li, J.; Stein, D.; McMullan, C.; Branton, D.; Aziz, M. J.; Golovchenko, J. A. Nature 2001, 412, 166.)) and in materials containing pores of nanometer dimensions (e.g., zeolite catalysts and skin) are of interest throughout chemistry and biology. It is generally recognized that transport selectivity, based on a chemical or physical property of the permeant, is often observed in pores when the size of the pore is sufficiently small that interactions between the pore surface and permeant influence local transport dynamics (“permeant” refers to a molecule or ion that passes through the pore). The rate of alkali metal ion transport through gramicidin channels, for instance, is highly dependent on metal ion radius, a consequence of the channel radius (˜2 Å) being comparable to the dehydrated ion radius ((a) Andersen, O. S.; Feldberg, S. W. J. Phys. Chem. 1996, 100, 4622; (b) Andersen, O. S. Biophys. J. 1983, 41, 147; (c) Andersen, O. S. Biophys. J. 1983, 41, 135). Longer range interactions over a few to tens of nanometers (e.g., electrostatic forces) between the pore surface and permeant can also lead to transport selectivity in pores of larger dimensions ((a) Daiguji, H.; Yang, P.; Majumdar, A. Nano Lett. 2004, 4, 137; (b) Karnik, R.; Fan, R.; Yue, M.; Li, D.; Yang, P.'; Majumdar, A. Nano Lett., 2005, 5, 943).
Developments over the past several decades in understanding pore transport mechanisms and the origins of transport selectivity have led to recent interest in the development of chemical and biological sensors based on selective transport through nanometer scale channels and pores. Protein ion channels, such as α-hemolysin, engineered or chemically modified to interact with a target analyte, are capable of detecting individual molecules by measuring the modulation of ionic current through the protein upon analyte binding (Meller, A. J. Phys. Condens. Matter 2003, 15, R581). The ability to observe molecule or particle transport dynamics within individual nanopores, rather than ensembled averaged results, has motivated fundamental research on pores employing biological as well as synthetic affinity pairs (Umezawa, Y.; Aoki, H. Anal. Chem. 2004, 76, 320 A).
In addition to biological pores, there have been significant advances in analytic detection employing synthetic pores in recent years, made largely possible by the rapid developments in methods and materials for nanoscale synthesis ((a) Jirage, K. B.; Hulteen, J. C.; Martin, C. R. Science 1997, 278, 655; (b) Harrell, C. C.; Lee, S. B.; Martin, C. R. Anal. Chem. 2003, 75, 6861 (c) Harrell, C. C.; Kohli, P. Siwy, Z.; Martin, C. R. J. Am. Chem. Soc. 2004, 126, 15646. (d) Fologea, D.; Gershow, M.; Ledden, B.; McNabb, D. S.; Golovchenko, J. A.; Li, Jiali Nano Lett. 2005, 5, 1905; (e) Fologea, D.; Gershow, M.; Uplinger, J; Thomas, B.; McNabb, D. S.; Li, Jiali Nano Lett. 2005, 5, 1734; (f) Chen, P.; Gu, J.; Brandin, E., Kin, Y.-R., Wang, Q.; Branton, D. Nano Lett., 2004, 4, 2293; (g) Storm, A. J.; Chen, J. H.; Ling, x. S.; Zandbergen, H. W.; Dekker, C. Nat. Mater. 2003, 2, 537; (h) Liu, N.; Dunphy, D. R.; Atanassov, P.; Bunge, S. D.; Chen, Z.; López, G. P.; Boyle, T. J.; Brinker, C. J. Nano Lett. 2004, 4, 551; (i) Fan, R. Karnik, R.; Yue, M. Li, D., Majumdar, A; Yang, P. Nano Lett. 2005, 5, 1633). For example, polycarbonate membranes that contain nanosize channels have been employed for the template synthesis of gold nanotubes, which can be subsequently functionalized for biosensor applications including the detection of DNA molecules (Heins, E. A.; Siwy, Z. S.; Baker, L. A.; Martin, C. R. Nano Lett., 2005, 5, 1824.). pH-switchable ion transport selectivity has been achieved by attachment of cysteine at the surface of the Au nanotubes (Lee, S. B.; Martin, C. R. Anal. Chem. 2001, 73, 768). Solid-state nanopores fabricated in Si3N4 membranes ((a) Fologea, D.; Gershow, M.; Ledden, B.; McNabb, D. S.; Golovchenko, J. A.; Li, Jiali Nano Lett. 2005, 5, 1905; (b) Fologea, D.; Gershow, M.; Uplinger, J; Thomas, B.; McNabb, D. S.; Li, Jiali Nano Lett. 2005, 5, 1734; (c) Chen, P.; Gu, J.; Brandin, E., Kin, Y.-R., Wang, Q.; Branton, D. Nano Lett., 2004, 4, 2293; (d) Storm, A. J.; Chen, J. H.; Ling, x. S.; Zandbergen, H. W.; Dekker, C. Nat. Mater. 2003, 2, 537; (e) Liu, N.; Dunphy, D. R.; Atanassov, P.; Bunge, S. D.; Chen, Z.; Lopez, G. P.; Boyle, T. J.; Brinker, C. J. Nano Lett. 2004, 4, 551) have been used for single molecule analysis and DNA detection, and silicon nanotubes have been integrated with microfluidic systems for DNA sensing (Fan, R. Karnik, R.; Yue, M. Li, D., Majumdar, A; Yang, P. Nano Lett. 2005, 5, 1633.) Carbon nanotubes (CNTs) have been employed as a nanoparticle Coulter counter (Ito, T.; Sun, L.; Crooks, R. M. Anal. Chem. 2003, 75, 2399). Aligned and chemically modified CNTs, incorporated into polymer films to created multichannel membrane structures, are also capable of reporting analyte binding (Majumber, M.; Chopra, N.; Hings, B. J. J. Am. Chem. Soc. 2005, 127, 9062).
The use of biological nanopores, for detection of single molecules has been in practice for two decades (see, e.g., Deamer, D. W., Branton, D., Acc. Chem. Res. 2002, 35, 817-825). For example, the biological protein nanopore α-hemolysin (αHL) from Staphylococcus aureus has proven to be ideal for single molecule detection, given the inner pore constriction diameter of 1.6 nm (Song, S., Hobaugh, M. R., Shustak, C., Cheley, S., Bayley, H., Govaux, J. E., Science, 1996, 274, 1859-1865).
The use of nanometer-scale electrodes has also attracted considerable interest as tools in fundamental research since the late 1980s. For example, nanoelectrodes have been employed in studies of fast electron-transfer reactions (Watkins, J. J.; Chen, J.; White, H. S.; Abruña, H. D.; Maisonhaute, E.; and Amatore, C. Anal. Chem. 2003, 75, 3962; Penner, R. M.; Heben, M. J.; Longin, T. L.; Lewis, N. S. Science 1990, 250, 1118), interfacial structure (Conyers, J. L. Jr.; White, H. S. Anal. Chem. 2000, 72, 4441; Chen, S.; Kucemak, A. J. Phys. Chem. B 2002, 106, 9396), single electron and single molecule electrochemistry (Fan, F-R. F.; Bard, A. J.; Science 1995, 267, 871; Fan, F-R, F.; Kwak, J.; Bard, A. J. J. Am. Chem. Soc. 1996, 118, 9669), as mimics of fuel cell catalysts (Chen, S.; Kucemak, A. J. Phys. Chem. B 2004, 108, 13984), and as analytical probes in bioelectrochemical measurements (Wightman, R. M. Science 2006, 311, 1570).
Methods of fabricating nanometer-sized electrodes can be found in several reports (Zoski, C. G. Electroanalysis 2002, 14, 1041; Watkins, J. J.; Zhang, B.; White, H. S. J. Chem. Edu. 2005, 82, 712; Arrigan, D. W. M. Analyst 2004, 129, 1157). Most frequently, the end of an electrochemically etched carbon fiber or metal wire is sealed into an insulating material (e.g., glass, wax, and polymers) leaving the tip of the fiber or wire exposed (Penner, R. M.; Heben, M. J.; Lewis, N. S. Anal. Chem. 1989, 61, 1630; Huang, W-H.; Pang, D-W.; Tong, H.; Wang, Z-L.; Cheng, J-K. Anal. Chem. 2001, 73, 1048; Hrapovic, S.; Luong, J. H. T. Anal. Chem. 2003, 75, 3308; Slevin, C. J.; Gray, N. J.; Macpherson, J. V.; Webb, M. A.; Unwin, P. R. Electrochem. Comm. 1999, 1, 282; Woo, D-H.; Kang, H.; Park, S-M. Anal. Chem. 2003, 75, 6732). Electrodes fabricated in this way generally have a hemispherical or conical shape shrouded by a thin layer of insulating material. The nature of the insulator can restrict the use of the electrode. For example, electrodes insulated with thin organic layers are simple to prepare, but their use is generally restricted to aqueous solutions, and they tend to exhibit prohibitively large capacitive currents in transient measurements due to the capacitance of the thin insulating layer (Watkins, J. J.; Chen, J.; White, H. S.; Abruña, H. D.; Maisonhaute, E.; and Amatore, C. Anal. Chem. 2003, 75, 3962).
Nanometer sized disk electrodes have been fabricated by pulling Pt wires embedded in glass capillaries with micro-pipette pullers and subsequently exposing a disk-shaped area of the metal using mechanical polishes or chemical etchants (Ballesteros Katemann, B.; Schuhmann, W. Electroanalysis 2002, 14, 22). The resulting glass-shrouded electrodes are durable and have favorable electrical properties. However, using this procedure, it is difficult to prepare electrodes with consistent sizes. Moreover, the use of costly pipette pullers is required. Although Shao et al. mention the monitoring of resistance during the polishing of glass-sealed Pt nano-electrodes (Shao, Y.; Mirkin, M. V.; Fish, G.; Kokotov, S.; Palanker, D.; Lewis, A. Anal. Chem. 1997, 69, 1627), no details of the methodology and instrumentation have been published.